Multiple sequence alignment - TraesCS4A01G075100 
Loading Multiple Alignment...
 
 BLAST Results  
BLAST Results - Input Sequence 
    
     Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this
        to extract flanking regions for cloning. If the result of the multiple sequence alignment is
        not as expected, these results could be used for further investigation. 
    
  
    
       
      qseqid 
      sseqid 
      percentage.identical 
      alignment.length 
      no.mismatch 
      no.gap.openings 
      qstart 
      qend 
      sstart 
      send 
      evalue 
      bitscore 
     
   
  
    
      0 
      TraesCS4A01G075100 
      chr4A 
      100.000 
      2579 
      0 
      0 
      1 
      2579 
      74578051 
      74575473 
      0 
      4763 
     
    
      1 
      TraesCS4A01G075100 
      chr4D 
      95.005 
      2102 
      90 
      8 
      1 
      2093 
      393123749 
      393121654 
      0 
      3286 
     
    
      2 
      TraesCS4A01G075100 
      chr4D 
      91.376 
      487 
      39 
      3 
      2094 
      2579 
      393116526 
      393116042 
      0 
      664 
     
    
      3 
      TraesCS4A01G075100 
      chr4B 
      94.646 
      990 
      47 
      4 
      929 
      1918 
      482779045 
      482778062 
      0 
      1530 
     
    
      4 
      TraesCS4A01G075100 
      chr4B 
      88.734 
      861 
      60 
      19 
      1 
      855 
      482779897 
      482779068 
      0 
      1018 
     
    
      5 
      TraesCS4A01G075100 
      chr4B 
      91.434 
      572 
      46 
      2 
      1978 
      2548 
      482778062 
      482777493 
      0 
      782 
     
   
    
 
BLAST Results - HSPs grouped 
    
     These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the
        BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are
        purely upstream or downstream may be removed if they don't overlap both primers. 
    
  
    
       
      query 
      scaffold 
      start 
      end 
      length 
      rev.comp 
      avg.bitscore 
      max.bitscore 
      avg.percent.identical 
      query.start 
      query.end 
      num_hsp 
      groupid 
      homo_length 
     
   
  
    
      0 
      TraesCS4A01G075100 
      chr4A 
      74575473 
      74578051 
      2578 
      True 
      4763 
      4763 
      100.000000 
      1 
      2579 
      1 
      chr4A.!!$R1 
      2578 
     
    
      1 
      TraesCS4A01G075100 
      chr4D 
      393121654 
      393123749 
      2095 
      True 
      3286 
      3286 
      95.005000 
      1 
      2093 
      1 
      chr4D.!!$R2 
      2092 
     
    
      2 
      TraesCS4A01G075100 
      chr4B 
      482777493 
      482779897 
      2404 
      True 
      1110 
      1530 
      91.604667 
      1 
      2548 
      3 
      chr4B.!!$R1 
      2547 
     
   
 
 
        
            
                
                     AutoCloner calculated primer pairs  
                     These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3),
                        whilst remaining within the specified product range where possible. 
                 
                
                    
                 
             
        
	Forward
		Primers 
	Reverse
		Primers 
	
  
    
      Position 
      MSA Position 
      Penalty 
      Sequence 
      TM 
      GC 
      Self any TH 
      Self end TH 
      Hairpin 
      End Stability 
      Orientation 
     
   
  
    
      60 
      61 
      0.098376 
      CGACGTCGAAGGTAGGAAGG 
      59.902 
      60.0 
      33.35 
      0.0 
      43.02 
      3.46 
      F 
     
   
 
	
  
    
      Position 
      MSA Position 
      Penalty 
      Sequence 
      TM 
      GC 
      Self any TH 
      Self end TH 
      Hairpin 
      End Stability 
      Orientation 
     
   
  
    
      2016 
      2028 
      0.032815 
      TTGTCGACAATGGCGAGTCA 
      59.967 
      50.0 
      26.53 
      4.19 
      38.59 
      3.41 
      R 
     
   
 
 
    
        
            
                 All possible primers  
                 Listed here are all possible primers based on the multiple sequence alignment and SNPs generated
                    previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work
                    during PCR or sequencing,
                    these could be used as alternatives. 
             
            
                
             
         
    
    
        Forward
            Primers 
        Reverse
            Primers 
    
    
		
  
    
      Position 
      MSA Position 
      Penalty 
      Sequence 
      TM 
      GC 
      Self any TH 
      Self end TH 
      Hairpin 
      End Stability 
     
   
  
    
      35 
      36 
      2.610859 
      CACCCCCAGCTGTACCCT 
      60.611 
      66.667 
      13.81 
      0.00 
      0.00 
      4.34 
     
    
      60 
      61 
      0.098376 
      CGACGTCGAAGGTAGGAAGG 
      59.902 
      60.000 
      33.35 
      0.00 
      43.02 
      3.46 
     
    
      284 
      285 
      2.203209 
      GGCGCCTCCGAATTCCAT 
      60.203 
      61.111 
      22.15 
      0.00 
      36.29 
      3.41 
     
    
      370 
      381 
      7.787725 
      ATGATTCGGTTTAGATGGTTTCTAC 
      57.212 
      36.000 
      0.00 
      0.00 
      36.65 
      2.59 
     
    
      381 
      392 
      2.103537 
      GGTTTCTACCGGCTTAAGCA 
      57.896 
      50.000 
      27.83 
      7.40 
      37.47 
      3.91 
     
    
      390 
      401 
      4.696899 
      ACCGGCTTAAGCAAGATTTAAC 
      57.303 
      40.909 
      27.83 
      7.10 
      44.36 
      2.01 
     
    
      394 
      405 
      5.273944 
      CGGCTTAAGCAAGATTTAACCATC 
      58.726 
      41.667 
      27.83 
      5.28 
      44.36 
      3.51 
     
    
      434 
      445 
      7.040132 
      GGACAGACAAGAAAAATTCTTCCATCT 
      60.040 
      37.037 
      2.47 
      4.33 
      46.62 
      2.90 
     
    
      450 
      462 
      9.823647 
      TTCTTCCATCTCAGTCTAATTAATCAC 
      57.176 
      33.333 
      0.00 
      0.00 
      0.00 
      3.06 
     
    
      547 
      559 
      2.246739 
      CGGATATGGCTGTGGCACG 
      61.247 
      63.158 
      13.77 
      9.03 
      41.84 
      5.34 
     
    
      571 
      583 
      3.893720 
      CTGTTCAAGTTCAACAGCATCC 
      58.106 
      45.455 
      6.71 
      0.00 
      43.18 
      3.51 
     
    
      590 
      602 
      2.840038 
      TCCATTGCCTTCTGAGCTAAGA 
      59.160 
      45.455 
      0.00 
      0.00 
      0.00 
      2.10 
     
    
      599 
      611 
      4.261994 
      CCTTCTGAGCTAAGATGAGTAGGC 
      60.262 
      50.000 
      14.37 
      0.00 
      0.00 
      3.93 
     
    
      670 
      682 
      0.611062 
      TCCTGGTCGGTCGATTCAGT 
      60.611 
      55.000 
      17.92 
      0.00 
      31.34 
      3.41 
     
    
      676 
      688 
      0.109458 
      TCGGTCGATTCAGTTCCACG 
      60.109 
      55.000 
      0.00 
      0.00 
      0.00 
      4.94 
     
    
      794 
      806 
      0.606604 
      TCTTACCGGGAGAAGCACAC 
      59.393 
      55.000 
      6.32 
      0.00 
      0.00 
      3.82 
     
    
      819 
      831 
      0.248289 
      CAAATTCTTGGGCTGCTGGG 
      59.752 
      55.000 
      0.00 
      0.00 
      0.00 
      4.45 
     
    
      900 
      912 
      5.407691 
      CACATGCATCTGTATCTGTATGACC 
      59.592 
      44.000 
      0.00 
      0.00 
      37.58 
      4.02 
     
    
      955 
      967 
      1.209019 
      GATCACATCACTCCCAGCAGT 
      59.791 
      52.381 
      0.00 
      0.00 
      0.00 
      4.40 
     
    
      975 
      987 
      2.353839 
      CAGCAACGCAAGCACCAC 
      60.354 
      61.111 
      0.00 
      0.00 
      45.62 
      4.16 
     
    
      1110 
      1122 
      4.736896 
      GGTGACTCGTCCGTGGCC 
      62.737 
      72.222 
      0.00 
      0.00 
      0.00 
      5.36 
     
    
      1329 
      1341 
      1.002366 
      GGTGCTACGTCATGAAGCTG 
      58.998 
      55.000 
      16.69 
      7.94 
      37.16 
      4.24 
     
    
      1435 
      1447 
      1.803117 
      GTAGTCGCCGACGGGAAAC 
      60.803 
      63.158 
      17.22 
      9.15 
      40.63 
      2.78 
     
    
      1665 
      1677 
      2.975732 
      TGCAAGCCAAATGTTGACAA 
      57.024 
      40.000 
      0.00 
      0.00 
      0.00 
      3.18 
     
    
      1725 
      1737 
      8.716646 
      AAATAAGAAATGAATAAAAAGGCCCG 
      57.283 
      30.769 
      0.00 
      0.00 
      0.00 
      6.13 
     
    
      1794 
      1806 
      0.544697 
      AAAGGAACGGCCGGATGTAT 
      59.455 
      50.000 
      31.76 
      8.61 
      43.43 
      2.29 
     
    
      1826 
      1838 
      4.038042 
      CCTTGAACTGTTTTCTTCTTCCCC 
      59.962 
      45.833 
      0.00 
      0.00 
      0.00 
      4.81 
     
    
      1832 
      1844 
      2.436542 
      TGTTTTCTTCTTCCCCTCGACA 
      59.563 
      45.455 
      0.00 
      0.00 
      0.00 
      4.35 
     
    
      1840 
      1852 
      2.105821 
      TCTTCCCCTCGACAAACAACAT 
      59.894 
      45.455 
      0.00 
      0.00 
      0.00 
      2.71 
     
    
      1845 
      1857 
      3.366273 
      CCCCTCGACAAACAACATGATTG 
      60.366 
      47.826 
      0.00 
      3.00 
      36.40 
      2.67 
     
    
      1929 
      1941 
      0.904865 
      TCTGAACCCTCACAGGCGAT 
      60.905 
      55.000 
      0.00 
      0.00 
      32.73 
      4.58 
     
    
      2016 
      2028 
      2.146342 
      CTCGCACATGTCAAAACCTCT 
      58.854 
      47.619 
      0.00 
      0.00 
      0.00 
      3.69 
     
    
      2025 
      2037 
      0.756294 
      TCAAAACCTCTGACTCGCCA 
      59.244 
      50.000 
      0.00 
      0.00 
      0.00 
      5.69 
     
    
      2032 
      2044 
      0.171231 
      CTCTGACTCGCCATTGTCGA 
      59.829 
      55.000 
      0.00 
      0.00 
      36.10 
      4.20 
     
    
      2046 
      2058 
      1.052124 
      TGTCGACAACACCCCTCCTT 
      61.052 
      55.000 
      17.62 
      0.00 
      31.20 
      3.36 
     
    
      2070 
      2082 
      2.045536 
      GGCCCTGGCTCAGTCTTG 
      60.046 
      66.667 
      8.29 
      0.00 
      41.60 
      3.02 
     
    
      2097 
      2109 
      3.367395 
      GGCCTTGCACTACTGGAATTTTC 
      60.367 
      47.826 
      0.00 
      0.00 
      0.00 
      2.29 
     
    
      2098 
      2110 
      3.255642 
      GCCTTGCACTACTGGAATTTTCA 
      59.744 
      43.478 
      0.00 
      0.00 
      0.00 
      2.69 
     
    
      2111 
      2123 
      5.708948 
      TGGAATTTTCAAATTAGGCACTCG 
      58.291 
      37.500 
      0.00 
      0.00 
      41.75 
      4.18 
     
    
      2154 
      2167 
      1.521450 
      ATCGGTGAACACGACTCGGT 
      61.521 
      55.000 
      2.98 
      0.00 
      43.78 
      4.69 
     
    
      2190 
      2203 
      4.412207 
      GCAAAAGTGACTTTGTCGAGTTT 
      58.588 
      39.130 
      11.83 
      0.00 
      38.35 
      2.66 
     
    
      2212 
      2225 
      2.031258 
      TTTCACAGGCACTCGACAAA 
      57.969 
      45.000 
      0.00 
      0.00 
      34.60 
      2.83 
     
    
      2220 
      2233 
      2.139917 
      GGCACTCGACAAACACATACA 
      58.860 
      47.619 
      0.00 
      0.00 
      0.00 
      2.29 
     
    
      2222 
      2235 
      3.002862 
      GGCACTCGACAAACACATACAAA 
      59.997 
      43.478 
      0.00 
      0.00 
      0.00 
      2.83 
     
    
      2223 
      2236 
      4.496673 
      GGCACTCGACAAACACATACAAAA 
      60.497 
      41.667 
      0.00 
      0.00 
      0.00 
      2.44 
     
    
      2224 
      2237 
      5.031578 
      GCACTCGACAAACACATACAAAAA 
      58.968 
      37.500 
      0.00 
      0.00 
      0.00 
      1.94 
     
    
      2226 
      2239 
      6.129457 
      GCACTCGACAAACACATACAAAAATC 
      60.129 
      38.462 
      0.00 
      0.00 
      0.00 
      2.17 
     
    
      2227 
      2240 
      6.084939 
      CACTCGACAAACACATACAAAAATCG 
      59.915 
      38.462 
      0.00 
      0.00 
      0.00 
      3.34 
     
    
      2261 
      2274 
      3.855950 
      CGTGTATAGGGAACTCGACAAAC 
      59.144 
      47.826 
      0.00 
      0.00 
      43.67 
      2.93 
     
    
      2262 
      2275 
      3.855950 
      GTGTATAGGGAACTCGACAAACG 
      59.144 
      47.826 
      0.00 
      0.00 
      43.67 
      3.60 
     
    
      2278 
      2291 
      4.165779 
      ACAAACGAAAAGTGCAAACAGAG 
      58.834 
      39.130 
      0.00 
      0.00 
      0.00 
      3.35 
     
    
      2295 
      2308 
      0.512952 
      GAGCGGCGCATTAATGGTAG 
      59.487 
      55.000 
      35.02 
      6.90 
      0.00 
      3.18 
     
    
      2298 
      2311 
      1.295792 
      CGGCGCATTAATGGTAGTGT 
      58.704 
      50.000 
      17.02 
      0.00 
      0.00 
      3.55 
     
    
      2356 
      2369 
      0.388907 
      GCACTCCGCAATGCAACAAT 
      60.389 
      50.000 
      5.91 
      0.00 
      41.65 
      2.71 
     
    
      2426 
      2439 
      3.181533 
      GCGAAACTCGACAATACCTTGAC 
      60.182 
      47.826 
      0.00 
      0.00 
      43.74 
      3.18 
     
    
      2430 
      2443 
      2.758979 
      ACTCGACAATACCTTGACGGAT 
      59.241 
      45.455 
      9.53 
      0.00 
      45.99 
      4.18 
     
    
      2433 
      2446 
      3.116300 
      CGACAATACCTTGACGGATGAG 
      58.884 
      50.000 
      3.01 
      0.00 
      43.56 
      2.90 
     
    
      2458 
      2471 
      3.696051 
      AGTGCCACATAGCATAACCTTTG 
      59.304 
      43.478 
      0.00 
      0.00 
      46.24 
      2.77 
     
    
      2475 
      2488 
      3.311322 
      CCTTTGTCGAGTGTTGCTTGTAA 
      59.689 
      43.478 
      0.00 
      0.00 
      0.00 
      2.41 
     
    
      2477 
      2490 
      2.479837 
      TGTCGAGTGTTGCTTGTAAGG 
      58.520 
      47.619 
      0.00 
      0.00 
      0.00 
      2.69 
     
    
      2484 
      2497 
      2.554032 
      GTGTTGCTTGTAAGGTGCTCAT 
      59.446 
      45.455 
      0.00 
      0.00 
      0.00 
      2.90 
     
    
      2548 
      2561 
      5.061560 
      GCAGTCTTTGTCGAGTTTCTATCTG 
      59.938 
      44.000 
      0.00 
      0.00 
      0.00 
      2.90 
     
    
      2549 
      2562 
      6.382608 
      CAGTCTTTGTCGAGTTTCTATCTGA 
      58.617 
      40.000 
      0.00 
      0.00 
      0.00 
      3.27 
     
    
      2550 
      2563 
      6.863645 
      CAGTCTTTGTCGAGTTTCTATCTGAA 
      59.136 
      38.462 
      0.00 
      0.00 
      0.00 
      3.02 
     
    
      2551 
      2564 
      7.061673 
      CAGTCTTTGTCGAGTTTCTATCTGAAG 
      59.938 
      40.741 
      0.00 
      0.00 
      35.89 
      3.02 
     
    
      2552 
      2565 
      6.309251 
      GTCTTTGTCGAGTTTCTATCTGAAGG 
      59.691 
      42.308 
      0.00 
      0.00 
      35.89 
      3.46 
     
    
      2553 
      2566 
      5.977489 
      TTGTCGAGTTTCTATCTGAAGGA 
      57.023 
      39.130 
      0.00 
      0.00 
      35.89 
      3.36 
     
    
      2554 
      2567 
      5.977489 
      TGTCGAGTTTCTATCTGAAGGAA 
      57.023 
      39.130 
      0.00 
      0.00 
      35.89 
      3.36 
     
    
      2555 
      2568 
      5.710984 
      TGTCGAGTTTCTATCTGAAGGAAC 
      58.289 
      41.667 
      0.00 
      4.02 
      35.51 
      3.62 
     
    
      2556 
      2569 
      5.477291 
      TGTCGAGTTTCTATCTGAAGGAACT 
      59.523 
      40.000 
      11.07 
      11.07 
      46.07 
      3.01 
     
    
      2561 
      2574 
      7.067496 
      AGTTTCTATCTGAAGGAACTCAACA 
      57.933 
      36.000 
      7.36 
      0.00 
      40.65 
      3.33 
     
    
      2562 
      2575 
      7.509546 
      AGTTTCTATCTGAAGGAACTCAACAA 
      58.490 
      34.615 
      7.36 
      0.00 
      40.65 
      2.83 
     
    
      2563 
      2576 
      7.993183 
      AGTTTCTATCTGAAGGAACTCAACAAA 
      59.007 
      33.333 
      7.36 
      0.00 
      40.65 
      2.83 
     
    
      2564 
      2577 
      8.787852 
      GTTTCTATCTGAAGGAACTCAACAAAT 
      58.212 
      33.333 
      4.68 
      0.00 
      38.49 
      2.32 
     
    
      2565 
      2578 
      8.924511 
      TTCTATCTGAAGGAACTCAACAAATT 
      57.075 
      30.769 
      0.00 
      0.00 
      38.49 
      1.82 
     
    
      2566 
      2579 
      8.924511 
      TCTATCTGAAGGAACTCAACAAATTT 
      57.075 
      30.769 
      0.00 
      0.00 
      38.49 
      1.82 
     
    
      2567 
      2580 
      9.354673 
      TCTATCTGAAGGAACTCAACAAATTTT 
      57.645 
      29.630 
      0.00 
      0.00 
      38.49 
      1.82 
     
    
      2568 
      2581 
      9.971922 
      CTATCTGAAGGAACTCAACAAATTTTT 
      57.028 
      29.630 
      0.00 
      0.00 
      38.49 
      1.94 
     
    
      2569 
      2582 
      8.877808 
      ATCTGAAGGAACTCAACAAATTTTTC 
      57.122 
      30.769 
      0.00 
      0.00 
      38.49 
      2.29 
     
    
      2570 
      2583 
      7.264947 
      TCTGAAGGAACTCAACAAATTTTTCC 
      58.735 
      34.615 
      8.44 
      8.44 
      38.49 
      3.13 
     
    
      2571 
      2584 
      6.940739 
      TGAAGGAACTCAACAAATTTTTCCA 
      58.059 
      32.000 
      15.90 
      0.00 
      38.49 
      3.53 
     
    
      2572 
      2585 
      7.041107 
      TGAAGGAACTCAACAAATTTTTCCAG 
      58.959 
      34.615 
      15.90 
      2.34 
      38.49 
      3.86 
     
    
      2573 
      2586 
      5.917462 
      AGGAACTCAACAAATTTTTCCAGG 
      58.083 
      37.500 
      15.90 
      0.00 
      35.87 
      4.45 
     
    
      2574 
      2587 
      5.660864 
      AGGAACTCAACAAATTTTTCCAGGA 
      59.339 
      36.000 
      15.90 
      0.00 
      35.87 
      3.86 
     
    
      2575 
      2588 
      5.985530 
      GGAACTCAACAAATTTTTCCAGGAG 
      59.014 
      40.000 
      10.78 
      5.34 
      33.96 
      3.69 
     
    
      2576 
      2589 
      6.406961 
      GGAACTCAACAAATTTTTCCAGGAGT 
      60.407 
      38.462 
      10.78 
      5.83 
      33.96 
      3.85 
     
    
      2577 
      2590 
      6.544928 
      ACTCAACAAATTTTTCCAGGAGTT 
      57.455 
      33.333 
      0.00 
      0.00 
      29.46 
      3.01 
     
    
      2578 
      2591 
      7.654022 
      ACTCAACAAATTTTTCCAGGAGTTA 
      57.346 
      32.000 
      0.00 
      0.00 
      29.46 
      2.24 
     
   
	 
    
		
  
    
      Position 
      MSA Position 
      Penalty 
      Sequence 
      TM 
      GC 
      Self any TH 
      Self end TH 
      Hairpin 
      End Stability 
     
   
  
    
      149 
      150 
      2.980233 
      GCCTTGCAGCTGACCGTT 
      60.980 
      61.111 
      20.43 
      0.00 
      0.00 
      4.44 
     
    
      284 
      285 
      3.982372 
      GAACTGATCGCCGCACCGA 
      62.982 
      63.158 
      0.00 
      0.00 
      41.98 
      4.69 
     
    
      370 
      381 
      3.442273 
      TGGTTAAATCTTGCTTAAGCCGG 
      59.558 
      43.478 
      24.30 
      16.17 
      41.18 
      6.13 
     
    
      381 
      392 
      5.648092 
      CGAGAAACTGGGATGGTTAAATCTT 
      59.352 
      40.000 
      0.00 
      0.00 
      0.00 
      2.40 
     
    
      390 
      401 
      1.815421 
      CCGCGAGAAACTGGGATGG 
      60.815 
      63.158 
      8.23 
      0.00 
      0.00 
      3.51 
     
    
      394 
      405 
      2.434359 
      GTCCCGCGAGAAACTGGG 
      60.434 
      66.667 
      8.23 
      0.00 
      43.36 
      4.45 
     
    
      434 
      445 
      5.817988 
      CGGACTCGTGATTAATTAGACTGA 
      58.182 
      41.667 
      0.00 
      0.00 
      0.00 
      3.41 
     
    
      450 
      462 
      1.332552 
      CGAAAACAAACCACGGACTCG 
      60.333 
      52.381 
      0.00 
      0.00 
      43.02 
      4.18 
     
    
      571 
      583 
      4.449131 
      TCATCTTAGCTCAGAAGGCAATG 
      58.551 
      43.478 
      0.86 
      0.00 
      0.00 
      2.82 
     
    
      590 
      602 
      0.761187 
      ATGCATGGTCGCCTACTCAT 
      59.239 
      50.000 
      0.00 
      0.00 
      0.00 
      2.90 
     
    
      599 
      611 
      0.308684 
      CCCGAATTCATGCATGGTCG 
      59.691 
      55.000 
      27.21 
      27.21 
      0.00 
      4.79 
     
    
      670 
      682 
      1.434555 
      CTGGAATACAACGCGTGGAA 
      58.565 
      50.000 
      23.00 
      5.25 
      0.00 
      3.53 
     
    
      676 
      688 
      2.939460 
      AATTGGCTGGAATACAACGC 
      57.061 
      45.000 
      0.00 
      0.00 
      0.00 
      4.84 
     
    
      819 
      831 
      7.261325 
      AGAAGAAAAGGAGAAAGAAAAAGTGC 
      58.739 
      34.615 
      0.00 
      0.00 
      0.00 
      4.40 
     
    
      896 
      908 
      1.403647 
      CGCTTTATCTGGACACGGTCA 
      60.404 
      52.381 
      6.41 
      0.00 
      33.68 
      4.02 
     
    
      900 
      912 
      2.876091 
      TCTTCGCTTTATCTGGACACG 
      58.124 
      47.619 
      0.00 
      0.00 
      0.00 
      4.49 
     
    
      968 
      980 
      2.283532 
      AGAGCGAGAGGTGGTGCT 
      60.284 
      61.111 
      0.00 
      0.00 
      45.11 
      4.40 
     
    
      975 
      987 
      1.431440 
      CAAGACCGAGAGCGAGAGG 
      59.569 
      63.158 
      0.00 
      0.00 
      40.82 
      3.69 
     
    
      1110 
      1122 
      1.514228 
      CGTGTCGTCGATGGACTGG 
      60.514 
      63.158 
      17.11 
      8.00 
      41.16 
      4.00 
     
    
      1569 
      1581 
      2.409651 
      GCTAGCTGCTAGACGCGT 
      59.590 
      61.111 
      34.43 
      13.85 
      43.27 
      6.01 
     
    
      1665 
      1677 
      5.201713 
      ACACAACCGATCGATCATATCTT 
      57.798 
      39.130 
      24.40 
      5.40 
      0.00 
      2.40 
     
    
      1706 
      1718 
      5.912955 
      CGATACGGGCCTTTTTATTCATTTC 
      59.087 
      40.000 
      0.84 
      0.00 
      0.00 
      2.17 
     
    
      1711 
      1723 
      4.888038 
      AACGATACGGGCCTTTTTATTC 
      57.112 
      40.909 
      0.84 
      0.00 
      0.00 
      1.75 
     
    
      1719 
      1731 
      2.188062 
      TTTTCAAACGATACGGGCCT 
      57.812 
      45.000 
      0.84 
      0.00 
      0.00 
      5.19 
     
    
      1747 
      1759 
      1.154225 
      CGGCTTGCACAAATCGACC 
      60.154 
      57.895 
      0.00 
      0.00 
      0.00 
      4.79 
     
    
      1794 
      1806 
      7.703058 
      AGAAAACAGTTCAAGGAAGAAGAAA 
      57.297 
      32.000 
      0.00 
      0.00 
      0.00 
      2.52 
     
    
      1826 
      1838 
      4.151258 
      AGCAATCATGTTGTTTGTCGAG 
      57.849 
      40.909 
      8.97 
      0.00 
      31.55 
      4.04 
     
    
      1832 
      1844 
      6.215845 
      GGTGTTAGAAGCAATCATGTTGTTT 
      58.784 
      36.000 
      8.88 
      8.88 
      0.00 
      2.83 
     
    
      1840 
      1852 
      3.678056 
      AGACGGTGTTAGAAGCAATCA 
      57.322 
      42.857 
      0.00 
      0.00 
      0.00 
      2.57 
     
    
      1845 
      1857 
      2.067013 
      GGACAAGACGGTGTTAGAAGC 
      58.933 
      52.381 
      0.00 
      0.00 
      0.00 
      3.86 
     
    
      1877 
      1889 
      1.413808 
      GGAGGTGAGGATAGGAGGCTT 
      60.414 
      57.143 
      0.00 
      0.00 
      0.00 
      4.35 
     
    
      1982 
      1994 
      4.944372 
      CGAGTGGCGGCCGTATCC 
      62.944 
      72.222 
      28.70 
      20.18 
      36.03 
      2.59 
     
    
      2016 
      2028 
      0.032815 
      TTGTCGACAATGGCGAGTCA 
      59.967 
      50.000 
      26.53 
      4.19 
      38.59 
      3.41 
     
    
      2025 
      2037 
      0.036306 
      GGAGGGGTGTTGTCGACAAT 
      59.964 
      55.000 
      31.81 
      16.35 
      40.65 
      2.71 
     
    
      2032 
      2044 
      0.182775 
      GTGACAAGGAGGGGTGTTGT 
      59.817 
      55.000 
      0.00 
      0.00 
      37.12 
      3.32 
     
    
      2097 
      2109 
      2.867429 
      CTTTGCCGAGTGCCTAATTTG 
      58.133 
      47.619 
      0.00 
      0.00 
      40.16 
      2.32 
     
    
      2098 
      2110 
      1.202348 
      GCTTTGCCGAGTGCCTAATTT 
      59.798 
      47.619 
      0.00 
      0.00 
      40.16 
      1.82 
     
    
      2111 
      2123 
      1.401539 
      GGACTCGACAAATGCTTTGCC 
      60.402 
      52.381 
      8.09 
      0.00 
      44.39 
      4.52 
     
    
      2161 
      2174 
      3.258123 
      ACAAAGTCACTTTTGCCAACAGT 
      59.742 
      39.130 
      0.00 
      0.00 
      40.80 
      3.55 
     
    
      2199 
      2212 
      2.224185 
      TGTATGTGTTTGTCGAGTGCCT 
      60.224 
      45.455 
      0.00 
      0.00 
      0.00 
      4.75 
     
    
      2212 
      2225 
      4.576216 
      TGGCAACGATTTTTGTATGTGT 
      57.424 
      36.364 
      0.00 
      0.00 
      42.51 
      3.72 
     
    
      2220 
      2233 
      2.619646 
      ACGGTACTTGGCAACGATTTTT 
      59.380 
      40.909 
      13.85 
      0.00 
      42.51 
      1.94 
     
    
      2222 
      2235 
      1.533731 
      CACGGTACTTGGCAACGATTT 
      59.466 
      47.619 
      13.85 
      0.00 
      42.51 
      2.17 
     
    
      2223 
      2236 
      1.153353 
      CACGGTACTTGGCAACGATT 
      58.847 
      50.000 
      13.85 
      0.00 
      42.51 
      3.34 
     
    
      2224 
      2237 
      0.034337 
      ACACGGTACTTGGCAACGAT 
      59.966 
      50.000 
      13.85 
      0.00 
      42.51 
      3.73 
     
    
      2226 
      2239 
      1.717194 
      ATACACGGTACTTGGCAACG 
      58.283 
      50.000 
      0.00 
      0.41 
      42.51 
      4.10 
     
    
      2227 
      2240 
      3.192466 
      CCTATACACGGTACTTGGCAAC 
      58.808 
      50.000 
      0.00 
      0.00 
      0.00 
      4.17 
     
    
      2261 
      2274 
      1.388888 
      CGCTCTGTTTGCACTTTTCG 
      58.611 
      50.000 
      0.00 
      0.00 
      0.00 
      3.46 
     
    
      2262 
      2275 
      1.758783 
      CCGCTCTGTTTGCACTTTTC 
      58.241 
      50.000 
      0.00 
      0.00 
      0.00 
      2.29 
     
    
      2265 
      2278 
      2.896801 
      CGCCGCTCTGTTTGCACTT 
      61.897 
      57.895 
      0.00 
      0.00 
      0.00 
      3.16 
     
    
      2278 
      2291 
      0.041312 
      CACTACCATTAATGCGCCGC 
      60.041 
      55.000 
      10.11 
      0.00 
      0.00 
      6.53 
     
    
      2295 
      2308 
      0.041312 
      GACGTGTTGCCATGTGACAC 
      60.041 
      55.000 
      0.00 
      11.38 
      40.91 
      3.67 
     
    
      2298 
      2311 
      1.333308 
      CAAAGACGTGTTGCCATGTGA 
      59.667 
      47.619 
      0.00 
      0.00 
      40.91 
      3.58 
     
    
      2343 
      2356 
      2.593775 
      CCTCGTTTATTGTTGCATTGCG 
      59.406 
      45.455 
      3.84 
      0.00 
      0.00 
      4.85 
     
    
      2356 
      2369 
      0.398696 
      ATGTGCCACACCCTCGTTTA 
      59.601 
      50.000 
      0.00 
      0.00 
      32.73 
      2.01 
     
    
      2389 
      2402 
      2.045926 
      CGCCTGGGAAGGAACTGG 
      60.046 
      66.667 
      0.00 
      0.00 
      40.86 
      4.00 
     
    
      2392 
      2405 
      0.250770 
      AGTTTCGCCTGGGAAGGAAC 
      60.251 
      55.000 
      0.00 
      0.00 
      0.00 
      3.62 
     
    
      2395 
      2408 
      1.741770 
      CGAGTTTCGCCTGGGAAGG 
      60.742 
      63.158 
      0.00 
      0.00 
      31.14 
      3.46 
     
    
      2423 
      2436 
      2.359169 
      GGCACTCCCTCATCCGTCA 
      61.359 
      63.158 
      0.00 
      0.00 
      0.00 
      4.35 
     
    
      2426 
      2439 
      1.976132 
      ATGTGGCACTCCCTCATCCG 
      61.976 
      60.000 
      19.83 
      0.00 
      42.63 
      4.18 
     
    
      2430 
      2443 
      0.909133 
      TGCTATGTGGCACTCCCTCA 
      60.909 
      55.000 
      19.83 
      7.53 
      41.05 
      3.86 
     
    
      2433 
      2446 
      2.222027 
      GTTATGCTATGTGGCACTCCC 
      58.778 
      52.381 
      19.83 
      5.29 
      45.36 
      4.30 
     
    
      2458 
      2471 
      2.221055 
      CACCTTACAAGCAACACTCGAC 
      59.779 
      50.000 
      0.00 
      0.00 
      0.00 
      4.20 
     
    
      2475 
      2488 
      2.076863 
      GTAAGCGTTTGATGAGCACCT 
      58.923 
      47.619 
      0.00 
      0.00 
      0.00 
      4.00 
     
    
      2477 
      2490 
      2.094417 
      GGAGTAAGCGTTTGATGAGCAC 
      59.906 
      50.000 
      0.00 
      0.00 
      0.00 
      4.40 
     
    
      2484 
      2497 
      1.968493 
      ACTCCTGGAGTAAGCGTTTGA 
      59.032 
      47.619 
      27.37 
      0.00 
      41.51 
      2.69 
     
    
      2533 
      2546 
      5.956642 
      AGTTCCTTCAGATAGAAACTCGAC 
      58.043 
      41.667 
      0.00 
      0.00 
      35.40 
      4.20 
     
    
      2548 
      2561 
      6.479990 
      CCTGGAAAAATTTGTTGAGTTCCTTC 
      59.520 
      38.462 
      14.93 
      2.27 
      36.35 
      3.46 
     
    
      2549 
      2562 
      6.156083 
      TCCTGGAAAAATTTGTTGAGTTCCTT 
      59.844 
      34.615 
      14.93 
      0.00 
      36.35 
      3.36 
     
    
      2550 
      2563 
      5.660864 
      TCCTGGAAAAATTTGTTGAGTTCCT 
      59.339 
      36.000 
      14.93 
      0.00 
      36.35 
      3.36 
     
    
      2551 
      2564 
      5.912892 
      TCCTGGAAAAATTTGTTGAGTTCC 
      58.087 
      37.500 
      9.28 
      9.28 
      36.00 
      3.62 
     
    
      2552 
      2565 
      6.573434 
      ACTCCTGGAAAAATTTGTTGAGTTC 
      58.427 
      36.000 
      0.00 
      0.00 
      0.00 
      3.01 
     
    
      2553 
      2566 
      6.544928 
      ACTCCTGGAAAAATTTGTTGAGTT 
      57.455 
      33.333 
      0.00 
      0.00 
      0.00 
      3.01 
     
    
      2554 
      2567 
      6.544928 
      AACTCCTGGAAAAATTTGTTGAGT 
      57.455 
      33.333 
      0.00 
      0.00 
      32.30 
      3.41 
     
   
	 
	
  
 
Based at the University of Bristol  with support from BBSRC .
 
 
AutoCloner maintained by Alex Coulton.